Answers

For Windows Store javascript/HTML app development, you can use the built-in "Windows Library for javascript" to handle most basic cases. and Visual Studio 2012 provides some Windows Store javascript project template which has included many pre-generated
code which demonstrate the general workflow and coding style of windows store javascript/html app.

And for 3rd party js library, you can surely use them (such as JQuery) to help on implementing some UI or function logics. But since the windows store app programming model has some difference from traditional web page based web applications, you need to
fully test the 3rd party js library when using them in your windows store app. The following MSDN references introduces something about the difference between Windows Store html/js app and normal web browser and web page based web app:

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For Windows Store javascript/HTML app development, you can use the built-in "Windows Library for javascript" to handle most basic cases. and Visual Studio 2012 provides some Windows Store javascript project template which has included many pre-generated
code which demonstrate the general workflow and coding style of windows store javascript/html app.

And for 3rd party js library, you can surely use them (such as JQuery) to help on implementing some UI or function logics. But since the windows store app programming model has some difference from traditional web page based web applications, you need to
fully test the 3rd party js library when using them in your windows store app. The following MSDN references introduces something about the difference between Windows Store html/js app and normal web browser and web page based web app: